Publications & Talks

Also available on Google Scholar

Peer-reviewed articles

2016

[81]  Cathelijne van der Wouden, Anne Cambon-Thomsen, Henk-Jan Guchelaar, Erika Cecchin, Ka-Chun Cheung, Cristina Lucía Dávila-Fajardo, Vera Deneer, Vita Dolzan, Magnus Ingelman-Sundberg, Siv Jönsson, Mats Karlsson, Marjolein Kriek, Christina Mitropoulou, George Patrinos, Munir Pirmohamed, Matthias Samwald, Elke Schaeffeler, Matthias Schwab, Daniela Steinberger, Julia Stingl, Gere Sunder-Plassmann, Giuseppe Toffoli, Richard Turner, Mandy van Rhenen, and Jesse Swen. “Implementing Pharmacogenomics in Europe: Design and Implementation Strategy of the Ubiquitous Pharmacogenomics Consortium” Clinical Pharmacology & Therapeutics  (accepted; journal article, impact factor 7,9)

[80] Matthias Samwald, Hong Xu, Kathrin Blagec, Philip E. Empey, Daniel C. Malone, Seid Mussa Ahmed, Patrick Ryan, Sebastian Hofer, and Richard D. Boyce. “Incidence of Exposure of Patients in the United States to Multiple Drugs for Which Pharmacogenomic Guidelines Are Available.” PLOS ONE 11, no. 10 (October 20, 2016): e0164972. doi:10.1371/journal.pone.0164972. (journal article, impact factor 3,5)

[79] Cathelijne H. van der Wouden, Jesse J. Swen, Matthias Samwald, Christina Mitropoulou, Matthias Schwab, and Henk-Jan Guchelaar. “A Brighter Future for the Implementation of Pharmacogenomic Testing.” European Journal of Human Genetics, August 31, 2016. doi:10.1038/ejhg.2016.116. (journal article, impact factor 4,3)

[78] Fan Zhu, Javier García-García, Eli Stahl, Abhishek Pratap, Gaurav Pandey, Dimitrios Pappas, Daniel Aguilar, Bernat Anton, Jaume Bonet, Ridvan Eksi, Oriol Fornés, Emre Guney, Hongdong Li, Manuel Alejandro Marín, Bharat Panwar, Joan Planas-Iglesias, Daniel Poglayen, Jing Cui, Andre O. Falcao, Christine Suver, Bruce Hoff, Venkat S. K. Balagurusamy, Donna Dillenberger, Elias Chaibub Neto, Thea Norman, Tero Aittokallio, Muhammad Ammad-ud-din, Chloe-Agathe Azencott, Víctor Bellón, Valentina Boeva, Kerstin Bunte, Himanshu Chheda, Lu Cheng, Jukka Corander, Michel Dumontier, Anna Goldenberg, Peddinti Gopalacharyulu, Mohsen Hajiloo, Daniel Hidru, Alok Jaiswal, Samuel Kaski, Beyrem Khalfaoui, Suleiman Ali Khan, Eric R. Kramer, Pekka Marttinen, Aziz M. Mezlini, Bhuvan Molparia, Matti Pirinen, Janna Saarela, Matthias Samwald, Véronique Stoven, Hao Tang, Jing Tang, Ali Torkamani, Jean-Phillipe Vert, Bo Wang, Tao Wang, Krister Wennerberg, Nathan E. Wineinger, Guanghua Xiao, Yang Xie, Rae Yeung, Xiaowei Zhan, Cheng Zhao, Members of the Rheumatoid Arthritis Challenge Consortium, Jeff Greenberg, Joel Kremer, Kaleb Michaud, Anne Barton, Marieke Coenen, Xavier Mariette, Corinne Miceli, Nancy Shadick, Michael Weinblatt, Niek de Vries, Paul P. Tak, Danielle Gerlag, Tom W. J. Huizinga, Fina Kurreeman, Cornelia F. Allaart, S. Louis Bridges Jr., Lindsey Criswell, Larry Moreland, Lars Klareskog, Saedis Saevarsdottir, Leonid Padyukov, Peter K. Gregersen, Stephen Friend, Robert Plenge, Gustavo Stolovitzky, Baldo Oliva, Yuanfang Guan, Lara M. Mangravite, S. Louis Bridges, Lindsey Criswell, Larry Moreland, Lars Klareskog, Saedis Saevarsdottir, Leonid Padyukov, Peter K. Gregersen, Stephen Friend, Robert Plenge, Gustavo Stolovitzky, Baldo Oliva, Yuanfang Guan and Lara M. Mangravite “Crowdsourced Assessment of Common Genetic Contribution to Predicting Anti-TNF Treatment Response in Rheumatoid Arthritis.” Nature Communications 7 (August 23, 2016): 12460. doi:10.1038/ncomms12460 (journal article, impact factor 11,3)

[77] Wolfgang Kuch, Christoph Rinner, Walter Gall and Matthias Samwald. “How Many Patients Could Benefit From Pre-Emptive Pharmacogenomic Testing and Decision Support? A Retrospective Study Based on Nationwide Austrian Claims Data.” Studies in Health Technology and Informatics 223 (2016): 253–58. doi:10.3233/978-1-61499-645-3-253 (conference article)

[76] Matthias Samwald, Kathrin Blagec, Sebastian Hofer and Robert R. Freimuth. “One man’s *1 is another man’s *13? Trouble with current nomenclatures in personalized medicine” Summer school Genomic Medicine – Bridging Research and the Clinic, May 3 – May 7 2016, Portorož, Slovenia (invited conference article) Book of Abstracts

[75] Matthias Samwald“Bridging theory and practice: Clinical decision support systems for personalized medicine”, Summer school Genomic Medicine – Bridging Research and the Clinic, May 3 – May 7 2016, Portorož, Slovenia (invited conference article) Book of Abstracts

[74] Kathrin Blagec, Katrina M. Romagnoli, Richard D. Boyce and Matthias Samwald. “Examining Perceptions of the Usefulness and Usability of a Mobile-Based System for Pharmacogenomics Clinical Decision Support: A Mixed Methods Study.” PeerJ 4 (February 8, 2016): e1671. doi:10.7717/peerj.1671 (journal article, impact factor 2,1)

[73] RC Kiefer, DK Sharma, Matthias Samwald, MK Linan D Sottara, KK Wix, Robert R. Freimuth. “Emerging Resources for Pharmacogenomic Clinical Decision Support.” Pacific Symposium on Biocomputing (PSB) 2016, January 4 – January 8 2016, Hawaii, USA (poster)

2015

[72] Matthias Samwald, Kathrin Blagec, Sebastian Hofer and Robert R. Freimuth. “Analysing the potential for incorrect haplotype calls with different pharmacogenomic assays in different populations: a simulation based on 1000 Genomes data.” Pharmacogenomics, September 30, 2015. doi:10.2217/pgs.15.108 (journal article, impact factor 3,2)

[71] Sebastian Hofer, Kathrin Blagec, Robert R. Freimuth and Matthias Samwald. Analysing the potential for incorrect haplotype calls with different pharmacogenomic assays in different populations: a simulation based on 1000 Genomes data.” ESPT 2015: Integration of Pharmacogenomics in clinical decision support, October 7 – 9, 2015, Budapest, Hungary (poster)

[70] Sebastian Hofer, Matthias Samwald. “A tool for rapid aggregation of eQTLs in human cells”  The European Human Genetics Conference 2015 (ESHG 2015),  June 6 – 9, Glasgow, UK (poster)

[69] Serkan Ayvaz, John Horn, Oktie Hassanzadeh, Qian Zhu, Johann Stan, Nicholas P. Tatonetti, Santiago Vilar, Mathias Brochhausen, Matthias Samwald, Majid Rastegar-Mojarad, Michel Dumontier, and Richard D. Boyce. “Toward a Complete Dataset of Drug–drug Interaction Information from Publicly Available Sources.” Journal of Biomedical Informatics 55 (June 2015): 206–17. doi:10.1016/j.jbi.2015.04.006. (journal article, impact factor 2,5)

[68] Alexander Pfundner, Tobias Schönberg, John Horn, Richard D Boyce and Matthias Samwald. “Utilizing the Wikidata System to Improve the Quality of Medical Content in Wikipedia in Diverse Languages: A Pilot Study.” Journal of Medical Internet Research 17, no. 5 (May 5, 2015): e110. doi:10.2196/jmir.4163. (journal article, impact factor 4,7)

[67] Matthias Samwald, Jose A. Miñarro Giménez, Richard D. Boyce, Robert R. Freimuth, Klaus-Peter Adlassnig and Michel Dumontier. „Pharmacogenomic Knowledge Representation, Reasoning and Genome-Based Clinical Decision Support Based on OWL 2 DL Ontologies.” BMC Medical Informatics and Decision Making 15, no. 1 (February 22, 2015): 12. doi:10.1186/s12911-015-0130-1. (journal article, impact factor 1,5)

2014

[66] Matthias Samwald, Veronika Stefanov, Georg Petz, Claus-Dieter Volko and Allan Hanbury. „Improving the Quality and Findability of Open Medical Information on the Web: Medical Wikidata and the FindMeEvidence Search Engine” Medicine 2.0’14 Europe, World Congress on Social Media, Mobile Apps, Internet / Web 2.0, October 8 – October 10, 2014, Torremolinos, Spain (conference article) link

[65] Jeroen De Bruin, Jose Miñarro-Giménez, Matthias Samwald and Oscar Marin Alonso. „Visualising topic networks in infection control using word vector analysis” Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (poster)

[64] Matthias Samwald, José Antonio Minarro-Giménez, Kathrin Blagec and Klaus-Peter Adlassnig. Towards a global IT system for personalized medicine: the Medicine Safety Code initiative Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (conference article)

[63] José Antonio Minarro-Giménez, Oscar Marín-Alonso and Matthias Samwald. „Exploring the application of deep learning techniques on medical text corpora” Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (conference article)

[62] Matthias Samwald and Allan Hanbury. „An open-source, mobile-friendly search engine for public medical knowledge” Medical Informatics Europe 2014 (MIE2014), Istanbul, Turkey (conference article)

[61] José Antonio Minarro-Giménez and Matthias Samwald. „An update on Genomic CDS, a complex ontology for pharmacogenomics and clinical decision support” OWL Reasoner Evaluation Workshop 2014 (ORE2014), Vienna, Austria (conference article)

[60] Jose Antonio Miñarro-Giménez, Kathrin Blagec, Richard D. Boyce, Klaus-Peter Adlassnig and Matthias Samwald. „An Ontology-Based, Mobile-Optimized System for Pharmacogenomic Decision Support at the Point-of-Care.” PLoS ONE 9, no. 5 (May 2, 2014): e93769. doi:10.1371/journal.pone.0093769. Open access article (journal article, impact factor 4,2)

[59] Serkan Ayvaz, Qian Zhu, Harry Hochheiser, Mathias Brochhausen, John Horn, Michel Dumontier, Matthias Samwald and Richard Boyce. „Drug-Drug Interaction Data Source Survey and Linking” AMIA Summit on Translational Bioinformatics, April 7 – April 9, San Francisco, USA(poster)

[58] Michel Dumontier, Christopher JO Baker, Joachim Baran, Alison Callahan, Leonid Chepelev, José Cruz-Toledo, Nicholas R. Del Rio, Geraint Duck, Laura I Furlong, Nichealla Keath, Dana Klassen, James P McCusker, Núria Queralt-Rosinach, Matthias Samwald, Natalia Villanueva-Rosales, Mark D Wilkinson and Robert Hoehndorf. „The Semanticscience Integrated Ontology (SIO) for Biomedical Research and Knowledge Discovery.“ Journal of Biomedical Semantics 5, no. 1 (March 6, 2014): 14. doi:10.1186/2041-1480-5-14. Open access article (journal article)

2013

[57] Matthias Samwald and Robert R Freimuth. „Making data on essential pharmacogenes available for every patient everywhere: the Medicine Safety Code initiative“ Pharmacogenomics 14, Nr. 13 (October 2013): 1529–1531. doi:10.2217/pgs.13.121. Open access article (journal article; invited editorial; impact factor 3,9)

[56] Niraj Aswani, Thomas Beckers, Erich Birngruber, Célia Boyer, Andreas Burner, Jakub Bystron, Khalid Choukri, Sarah Cruchet, Hamish Cunningham, Jan Dedek, Ljiljana Dolamic, René Donner, Sebastian Dungs, Ivan Eggel, Antonio Foncubierta-Rodriguez, Norbert Fuhr, Adam Funk, Alba Garcia Seco de Herrera, Arnaud Gaudinat, Georgi Georgiev, Julien Gobeill, Lorraine Goeuriot, Paz Gomez, R. Mark Greenwood, Manfred Gschwandtner, Allan Hanbury, Jan Hajic, Jaroslava Hlavácová, Markus Holzer, Gareth J. F. Jones, Blanca Jordan, Matthias Jordan, Klemens Kaderk, Franz Kainberger, Liadh Kelly, Sascha Kriewel, Marlene Kritz, Georg Langs, Nolan Lawson, Dimitrios Markonis, Iván Martínez, Vassil Momtchev, Alexandre Masselot, Hélène Mazo, Henning Müller, João Palotti, Pavel Pecina, Konstantin Pentchev, Deyan Peychev, Natalia Pletneva, Diana Pottecher, Angus Roberts, Patrick Ruch, Alexander Sachs, Matthias Samwald, Priscille Schneller, Veronika Stefanov, Miguel Angel Tinte, Zdenka Uresová, Alejandro Vargas and Dina Vishnyakova. „Khresmoi-Multilingual Semantic Search of Medical Text and Images.“ Studies in Health Technology and Informatics 192 (2013): 1266.

[55] Veronika Stefanov, Alexander Sachs, Marlene Kritz, Matthias Samwald, Manfred Gschwandtner and Allan Hanbury. „A Formative Evaluation of a Comprehensive Search System for Medical Professionals.“ In Information Access Evaluation. Multilinguality, Multimodality, and Visualization, edited by Pamela Forner, Henning Müller, Roberto Paredes, Paolo Rosso, and Benno Stein, 81–92. Lecture Notes in Computer Science 8138. Springer Berlin Heidelberg, 2013. link (conference article)

[54] Matthias Samwald „Genomic CDS: an example of a complex ontology for pharmacogenetics and clinical decision support“ OWL Reasoner Evaluation Workshop 2013 (ORE2013), July 22, Ulm, Germany (conference article)

[53] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury „Physicians searching the web for medical question answering: A European survey and local user studies“ Medinfo2013, August 20-23, Copenhagen, Denmark (poster)

[52] Matthias Samwald, Robert Freimuth, Joanne S. Luciano, Simon Lin, Robert L. Powers, M. Scott Marshall, Klaus-Peter Adlassnig, Michel Dumontier, Richard D. Boyce. „An RDF/OWL Knowledge Base for Query Answering and Decision Support in Clinical Pharmacogenetics“ Medinfo2013, August 20-23, Copenhagen, Denmark (conference article) Open-access preprint version

[51] Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury, Matthias Samwald. „Utilisation and perceived problems of online medical resources and search tools among different groups of European physicians“ Journal of Medical Internet Research 15, no. 6 (2013): e122. Open-access article (journal article, impact factor 4,7)

[50] Matthias Samwald. „Semantically Enabling Genetic Medicine to Facilitate Patients and Guidelines Matching and Enhanced Clinical Decision Support“ Proceedings of the Conference on Semantics in Healthcare and Life Sciences 2013 (CSHALS 2013), February 28, 2013, Cambridge/Boston, Massachusetts, USA (conference article)
Slides

[49] Toshiaki Katayama, Mark D. Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal, Erick Antezana, Kazuharu Arakawa, Bruno Aranda, Francois Belleau, Jerven Bolleman, Raoul Jean Bonnal, Brad Chapman, Peter Cock, Tore Eriksson, Paul Gordon, Naohisa Goto, Kazuhiro Hayashi, Heiko Horn, Ryosuke Ishiwata, Eli Kaminuma, Arek Kasprzyk, Hideya Kawaji, Nobuhiro Kido, Young Joo Kim, Akira R Kinjo, Fumikazu Konishi, Kyung-Hoon Kwon, Alberto Labarga, Anna-Lena Lamprecht, Yu Lin, Pierre Lindenbaum, Luke McCarthy, Hideyuki Morita, Katsuhiko Murakami, Koji Nagao, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Pjotr Prins, Taro L Saito, Matthias Samwald, Venkata P Satagopam, Yasumasa Shigemoto, Richard Smith, Andrea Splendiani, Hideaki Sugawara, James Taylor, Rutger Vos, David Withers, Chisato Yamasaki, Christian M Zmasek, Shoko Kawamoto, Kosaku Okubo, Kiyoshi Asai, Toshihisa Takagi. „The 3rd DBCLS BioHackathon: Improving Life Science Data Integration with Semantic Web Technologies.“ Journal of Biomedical Semantics 4, no. 1 (February 11, 2013): 6. doi:10.1186/2041-1480-4-6.

[48] Matthias Samwald, Klaus-Peter Adlassnig. „Pharmacogenomics in the pocket of every patient? A prototype based on Quick Response (QR) codes“ Journal of the American Medical Informatics Association 20, no. 3 (January 5, 2013): 409–412. http://dx.doi.org/10.1136/amiajnl-2012-001275 (journal article; impact factor 3,6) Open access preprint version

2012

[47] Matthias Samwald, Zhan Ye, Daniel A Vasco, Steven Schrodi, Murray Brilliant, Simon Lin. „Pharmacogenomics in the Pocket of Every Patient? – A Prototype Card with Quick Response (QR) CodeCritical Assessment of Massive Data Analysis 2012 (CAMDA2012), co-located with the 20th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2012) (conference article)

[46] Gökhan Karakülah, Asli Suner, Klaus-Peter Adlassnig, Matthias Samwald. „A data-driven living review for pharmacogenomic decision support in cancer treatment Studies in Health Technology and Informatics 180 (2012): 688–692.(conference article)

[45] Niraj Aswani, Thomas Beckers, Erich Birngruber, Célia Boyer, Andreas Burner, Jakub Bystron, Khalid Choukri, Sarah Cruchet, Hamish Cunningham, Jan Dedek, Ljiljana Dolamic, René Donner, Sebastian Dungs, Ivan Eggel, Antonio Foncubierta-Rodríguez, Norbert Fuhr, Adam Funk, Alba García Seco de Herrera, Arnaud Gaudinat, Georgi Georgiev, Julien Gobeill, Lorraine Goeuriot, Paz Gómez, Mark Greenwood, Manfred Gschwandtner, Allan Hanbury, Jan Hajic, Jaroslava Hlavácová, Markus Holzer, Gareth Jones, Blanca Jordan, Matthias Jordan, Klemens Kaderk, Franz Kainberger, Liadh Kelly, Sascha Kriewel, Marlene Kritz, Georg Langs, Nolan Lawson, Dimitrios Markonis, Ivan Martinez, Vassil Momtchev, Alexandre Masselot, Hélène Mazo, Henning Müller, Pavel Pecina, Konstantin Pentchev, Deyan Peychev, Natalia Pletneva, Diana Pottecherc, Angus Roberts, Patrick Ruch, Matthias Samwald, Priscille Schneller, Veronika Stefanov, Miguel A. Tinte, Zdenka Urešová, Alejandro Vargas, and Dina Vishnyakova. „Khresmoi: Multimodal Multilingual Medical Information Search“ Medical Informatics Europe 2012 (MIE2012) (poster and presentation booth)

[44] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Allan Hanbury. A curated index of high-quality web resources for medical practitionersMedical Informatics Europe 2012 (MIE2012) (poster)

[43] Matthias Samwald, Karsten Fehre, Jeroen de Bruin, and Klaus-Peter Adlassnig. „The Arden Syntax Standard for Clinical Decision Support: Experiences and Directions.“ Journal of Biomedical Informatics 45, no. 4 (August 2012): 711–718 (journal article; impact factor 1,8) Open access preprint version

[42] M. Scott Marshall, Richard Boyce, Helena F. Deus, Jun Zhao, Egon L. Willighagen, Matthias Samwald, Elgar Pichler, Janos Hajagos, Eric Prud’hommeaux, and Susie Stephens. „Emerging Practices for Mapping and Linking Life Sciences Data Using RDF — A Case Series.“ Web Semantics: Science, Services and Agents on the World Wide Web 14 (July 2012): 2–13. (journal article, impact factor 2,8)

[41] Matthias Samwald, Adrien Coulet, Iker Huerga, Robert L Powers, Joanne S. Luciano, Robert R. Freimuth, Frederick Whipple, Elgar Pichler, Eric Prud’hommeaux, Michel Dumontier, M. Scott Marshall. „Semantically enabling pharmacogenomic data for the realization of personalized medicine“ Pharmacogenomics 13, no. 2 (January 2012): 201–212.(journal article; impact factor 3,9) Open access preprint version

[40] Matthias Samwald, Adrien Coulet, Robert R. Freimuth, Iker Huerga, Joanne Luciano, Elgar Pichler, Robert L. Powers, Eric Prud’hommeaux, Frederick Whipple, Michael Marshall, und Michel Dumontier. „An informatics infrastructure for translating pharmacogenomic knowledge into clinical practice“ In 2012 AMIA Summit on Translational Bioinformatics, 2012 Joint Summits on Translational Science, San Francisco California, Parc 55 Hotel San Francisco, March 19, 2012 – March 23, 2012 Manuscript ID AMIA-077-T2012 (conference article)

2011

[39] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury. „An open, trustworthy and multilingual search engine for medical practitioners“ In 23rd International Conference of the European Federation for Medical Informatics (MIE2011), User Centred Networked Health Care – A. Moen et al. (Eds.), MIE 2011 / CD / Short Communications, 2011 (conference article)

[38] Matthias Samwald, Holger Stenzhorn, Michel Dumontier, M. Scott Marshall, Joanne Luciano, Klaus-Peter Adlassnig. „Towards an interoperable information infrastructure providing decision support for genomic medicine“ Studies in Health Technology and Informatics 169 (2011): 165-169. Proceedings of Medical Informatics Europe 2011 (MIE2011). (conference article)
PDF, Link to publisher

[37] Matthias Samwald, Marlene Kritz, Manfred Gschwandtner, Veronika Stefanov, Allan Hanbury. „Towards an open, trustworthy and multilingual search engine for medical practitioners: News from the European Khresmoi project“ In Schreier, G., Hayn, D. & Ammenwerth, E. (Eds.) Tagungsband der eHealth2011 – Health Informatics meets eHealth – von der Wissenschaft zur Anwendung und zurück, Grenzen überwinden – Continuity of Care, 26.–27. Mai 2011, Wien, Österreichische Computer Gesellschaft, Wien, 135 – 140 (conference article)
PDF

[36] Matthias Samwald, Anja Jentzsch, Christopher Bouton, Claus Stie Kallesøe, Egon Willighagen, Janos Hajagos, M. Scott Marshall, Eric Prud’hommeaux, Oktie Hassanzadeh, Elgar Pichler, Susie Stephens. „Linked open drug data for pharmaceutical research and development“ Journal of Cheminformatics 3, no. 1 (2011): 19. (journal article; impact factor 3,4)
Read article at BioMed Central

[35] Joanne S. Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine Denney, Christopher Domarew, Thomas Gambet, Lee Harland, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, Timothy Lebo, M. Scott Marshall, James P. McCusker, Deborah L. McGuiness, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud?hommeaux, Matthias Samwald, Lynn Schriml, Petev J. Tonellato, Patricia L. Whetzel, Jun Zhao, Susie Stephens, Michel Dumontier. „The Translational Medicine Ontology and Knowledge Base: Driving personalized medicine by bridging the gap between bench and bedside“ Journal of Biomedical Semantics 2, no. 2 (2011): S1. (journal article)
Read article at BioMed Central

[34] Joanne S. Luciano, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Tim Clark, Christine Denney, Christine Domarew, Thomas Gambet, Anja Jentzsch, Vipul Kashyap, Peter Kos, Julia Kozlovsky, M. Scott Marshall, James P. McCusker, Deborah L. McGuiness, Timothy Lebo, Chimezie Ogbuji, Elgar Pichler, Robert L. Powers, Eric Prud’hommeaux, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Patricia L. Wletzel, Jun Zhao, Susie Stephens, Michel Dumontier. „The Translational Medicine Ontology and Knowledge Base: Using Semantic Web Technology in Personalized Medicine for Data Integration“ In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 7, 2011. (conference article)
Conference proceedings

[33] Matthias Samwald, Jun Zhao, Michel Dumontier, M. Scott Marshall, Kei Cheung, Joanne S. Luciano. „Translating ethnopharmacological findings into novel drug leads: the potential roles of linked open data and ontologies“ In Proceedings of the AMIA Summit on Translational Bioinformatics, San Francisco, CA, March 7, 2011. (poster)
Conference proceedings

2010

[32] Helena Deus, Jun Zhao, Satya Sahoo, Matthias Samwald, Eric Prud’hommeaux, Michael Miller, M.Scott Marshall, Kei-Hoi Cheung. “Provenance of Microarray Experiments for a Better Understanding of Experiment Results” Proceedings of Second International Workshop on the role of Semantic Web in Provenance Management (SWPM-2010), Shanghai, China (conference article)

[31] Matthias Samwald, Michel Dumontier, Jun Zhao, Joanne Luciano, M Scott Marshall, Kei-Hoi Cheung. “Integrating findings from traditional medicine into modern pharmaceutical research: the potential role of linked open data” Chinese Medicine 5, No. 1 (2010): 43. (journal article)
Read article at BioMed Central

[30] Emek Demir, Michael P Cary, Suzanne Paley, Ken Fukuda, Christian Lemer, Imre Vastrik, Guanming Wu, Peter D’Eustachio, Carl Schaefer, Joanne Luciano, Frank Schacherer, Irma Martinez-Flores, Zhenjun Hu, Veronica Jimenez-Jacinto, Geeta Joshi-Tope, Kumaran Kandasamy, Alejandra C Lopez-Fuentes, Huaiyu Mi, Elgar Pichler, Igor Rodchenkov, Andrea Splendiani, Sasha Tkachev, Jeremy Zucker, Gopal Gopinath, Harsha Rajasimha, Ranjani Ramakrishnan, Imran Shah, Mustafa Syed, Nadia Anwar, Özgün Babur, Michael Blinov, Erik Brauner, Dan Corwin, Sylva Donaldson, Frank Gibbons, Robert Goldberg, Peter Hornbeck, Augustin Luna, Peter Murray-Rust, Eric Neumann, Oliver Reubenacker, Matthias Samwald, Martijn van Iersel, Sarala Wimalaratne, Keith Allen, Burk Braun, Michelle Whirl-Carrillo, Kei-Hoi Cheung, Kam Dahlquist, Andrew Finney, Marc Gillespie, Elizabeth Glass, Li Gong, Robin Haw, Michael Honig, Olivier Hubaut, David Kane, Shiva Krupa, Martina Kutmon, Julie Leonard, Debbie Marks, David Merberg, Victoria Petri, Alex Pico, Dean Ravenscroft, Liya Ren, Nigam Shah, Margot Sunshine, Rebecca Tang, Ryan Whaley, Stan Letovksy, Kenneth H Buetow, Andrey Rzhetsky, Vincent Schachter, Bruno S Sobral, Ugur Dogrusoz, Shannon McWeeney, Mirit Aladjem, Ewan Birney, Julio Collado-Vides, Susumu Goto, Michael Hucka, Nicolas Le Novère, Natalia Maltsev, Akhilesh Pandey, Paul Thomas, Edgar Wingender, Peter D Karp, Chris Sander, Gary D Bader. “The BioPAX community standard for pathway data sharing.” Nature Biotechnology 28, Nr. 9 (9, 2010): 935-942. (journal article; impact factor 29,5)
Read article in Nature Biotechnology

[29] Kei-Hoi Cheung, Matthias Samwald, Raymond K. Auerbach, Mark B. Gerstein. “Structured digital tables on the Semantic Web: toward a structured digital literature” Nature Molecular Systems Biology 6 (August 24, 2010): 403. (journal article; impact factor 12,2)
Read article in Nature Molecular Systems Biology

[28] Michel Dumontier, Bosse Andersson, Colin Batchelor, Christine Denney, Christopher Domarew, Anja Jentzsch, Joanne Luciano, Elgar Pichler, Eric Prud’hommeaux, Patricia Whetzel, Olivier Bodenreider, Tim Clark, Lee Harland, Vipul Kashyap, Peter Kos, Julia Kozlovsky, James McGurk, Chimezie Ogbuji, Matthias Samwald, Lynn Schriml, Peter J. Tonellato, Jun Zhao, Susie Stephens. “The Translational Medicine Ontology: Driving personalized medicine by bridging the gap from bedside to bench”Bio-Ontologies 2010, Proceedings of the 13th Annual Bio-Ontologies Meeting, Boston, USA (conference article)

[27] Patricia L. Whetzel, Colin Batchelor, Elgar Pichler, Bosse Andersson, Olivier Bodenreider, Tim Clark, Christopher Domarew, Michel Dumontier, Anja Jentzsch, Vipul Kashyap, Julia Kozlovsky, Joanne Luciano, Chimezie Ogbuji, Matthias Samwald, Jun Zhao, Susie Stephens. “Translational Medicine Ontology: A Patient-Centric Ontology for Drug Development and Clinical Practice” Proceedings of the Summit on Translational Bioinformatics 2010, San Francisco, USA. (poster)

[26] Matthias Samwald, Holger Stenzhorn. “Establishing a distributed system for the simple representation and integration of diverse scientific assertions.” Journal of Biomedical Semantics 1, Nr. 1 (2010): S5. (journal article)
Read article at BioMed Central

[25] Matthias Samwald, Huajun Chen, Alan Ruttenberg, Ernest Lim, Luis Marenco, Perry Miller, Gordon Shepherd, Kei-Hoi Cheung. “Semantic SenseLab: implementing the vision of the Semantic Web in neuroscience” Artificial Intelligence in Medicine 48, no. 1 (January 2010): 21-28. (journal article; impact factor 1,96)
Read article in Artificial Intelligence in Medicine

2009

[24] Anita de Waard, Simon Buckingham Shum, Annamaria Carusi, Jack Park, Matthias Samwald, Ágnes Sándor. “Hypotheses, Evidence and Relationships: The HypER Approach for Representing Scientific Knowledge Claims” Proceedings of the Workshop on Semantic Web Applications in Scientific Discourse (SWASD 2009), co-located with the 8th International Semantic Web Conference (ISWC-2009). (conference article)
Conference Proceedings

[23] Matthias Samwald, Holger Stenzhorn. “Simple, ontology-based representation of biomedical statements through fine-granular entity tagging and new web standards” Bio-Ontologies 2009, co-located with ISMB2009. (conference article)
Article PDF, Presentation PDF

[22] Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud’hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke.A Journey to Semantic Web Query Federation in Life Sciences“ BMC Bioinformatics, 10, no. Suppl 10 (2009): S10 (journal article; impact factor 3,78)
Read article at BioMed Central

[21] Kei-Hoi Cheung, Ernest Lim, Matthias Samwald, Huajun Chen, Luis Marenco, Matthew E. Holford, Thomas M. Morse, Pradeep Mutalik, Gordon M. Shepherd, Perry L. Miller. Approaches to Neuroscience Data IntegrationBriefings in Bioinformatics, 10, no. 4 (July 2009): 345-353 (journal article; impact factor 4,63)
Read article at Oxford Journals

[20] Alan Ruttenberg, Jonathan A. Rees, Matthias Samwald, M. Scott Marshall. “Life sciences on the semantic web: the neurocommons and beyond” Briefings in Bioinformatics, 10, no. 2 (March 2009): 193-204 (journal article; impact factor 4,63)
Read article at Oxford Journals

[19] Anja Jentzsch, Jun Zhao, Oktie Hassanzadeh, Kei-Hoi Cheung, Matthias Samwald, Bo Andersson. “Linking Open Drug Data” In Proceedings of Linking Open Data Triplification Challenge at the I-Semantics 2009, 2009. (conference paper)
Article PDF

[18] Jun Zhao, Anja Jentzsch, Matthias Samwald, Kei-Hoi Cheung. „Linked Data for Connecting Traditional Chinese Medicine and Western Medicine” The Sixth International Workshop of Data Integration in the Life Sciences (Poster&Demo), Manchester, UK, 2009 (poster)

[17] Christine Denney, Bosse Andersson, Colin Batchelor, Olivier Bodenreider, Sam Cheng, John Hart, John Hill, Joanne Luciano, John Madden, Mark Musen, Elgar Pichler, Matthias Samwald, Sándor Szalma, Lynn Schriml, David Sedlock, Larisa Soldatova, Koji Sonoda, David Statham, Holger Stenzhorn, Trish Whetzel, Elizabeth Wu, Susie Stephens. Creating a Translational Medicine Ontology” The Sixth International Workshop of Data Integration in the Life Sciences (Poster&Demo), Manchester, UK, 2009 (poster)

[16] Christine Denney, Colin Batchelor, Olivier Bodenreider, Sam Cheng, John Hart, Jon Hill, John Madden, Mark Musen, Elgar Pichler, Matthias Samwald, Sándor Szalma, Lynn Schriml, David Sedlock, Larisa Soldatova, Koji Sonoda, David Statham, Patricia L. Whetzel, Elizabeth Wu, Susie Stephens. Creating a Translational Medicine Ontology” Proceedings of the First International Conference on Biomedical Ontology (ICBO 2009) 2009:164 (poster)

[15] Matthias Samwald, Ernest Lim, Peter Masiar, Luis Marenco, Huajun Chen, Thomas Morse, Pradeep Mutalik, Gordon Shepherd, Perry Miller, Kei-Hoi Cheung. Entrez Neuron RDFa: a pragmatic Semantic Web application for data integration in neuroscience researchStudies in Health Technology and Informatics/150 (2009): 317-321. Presented at the International Conference of the European Federation for Medical Informatics, 2009(conference article)
Link, Article PDF

[14] Alexandre Passant, Matthias Samwald, John Breslin, Stefan Decker. “Federating Distributed Social Data to Build an Interlinked Online Information Society.” In Proceedings of the WebSci’09: Society On-Line, 2009. (conference article)
Link, Article PDF

2008

[12] Matthias Samwald, Klaus-Peter Adlassnig. “The bio-zen plus ontology.” Applied Ontology 3, no. 4 (Januar 1, 2008): 213-217. (journal article)
Link

[11] Holger Stenzhorn, Kavitha Srinivas, Matthias Samwald, Alan Ruttenberg. “Simplifying Access to Large-Scale Health Care and Life Sciences Datasets.” In Proceedings of the 5th European Semantic Web Conference (ESWC2008). Tenerife, Spain: Springer, 2008. (conference article)

[10] Matthias Samwald, Kei-Hoi Cheung. “Experiences with the conversion of SenseLab databases to RDF/OWL (W3C Interest Group Note).” World Wide Web Consortium, 6, 2008. http://www.w3.org/TR/hcls-senselab/. (W3C interest group note)

[9] Sebastian Schaffert, Julia Eder, Matthias Samwald, Andreas Blumauer. “KiWi – Knowledge in a Wiki.” 5th European Semantic Web Conference (ESWC2008), Tenerife, Spain, 6, 2008. (poster)

[8] Christian Morbidoni, Danh Le Phuoc, Axel Polleres, Matthias Samwald, Giovanni Tummarello. “Previewing Semantic Web Pipes.” In Proceedings of the 5th European Semantic Web Conference (ESWC2008). Tenerife, Spain: Springer, 2008. (conference article)

2007

[7] Alan Ruttenberg, Tim Clark, William Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, et al. “Advancing translational research with the Semantic Web.” BMC Bioinformatics 8 Suppl 3 (2007): S2. doi:1471-2105-8-S3-S2. (journal article, impact factor 3.43)
Read article at BioMed Central Selected by Faculty of 1000

[6] Matthias Samwald, William Bug, Jonathan Rees, Chris Mungall, John Barkley, Ray Hookway, et al. “The Semantic Web Health Care and Life Sciences Interest Group work in progress: A large scale, OBO inspired, repository of biological knowledge based on Semantic Web technologies.” (Poster) International Conference on Intelligent Systems for Molecular Biology (ISMB2007), Vienna, Austria, 2007. (poster)

2006

[4] Matthias Samwald. “Classes Versus Individuals: Fundamental Design Issues for Ontologies on the Biomedical Semantic Web.” In Proceedings of the European Federation for Medical Informatics, Special Topic Conference. Timisoara, Romania, 2006. (conference article)
Article PDF

[3] Matthias Samwald, Isabella Hinterleitner, Klaus-Peter Adlassnig. “Semantic web technology for database integration in neuroscience.” In FENS Forum Abstracts, 3: Vienna, Austria, 2006. (conference article)

[2] Matthias Samwald, Alan Ruttenberg. “Representation and resolution of digital resources on the semantic web – an ontology-based approach.” Athens, Georgia, USA, 2006. (conference article)

2005

[1] Matthias Samwald, Klaus-Peter Adlassnig. “Bringing Neuroscience to the Semantic Web: The Semantic Synapse Project.” In Proceedings of the International Conference on Intelligent Agents, Web Technologies & Internet Commerce. Vienna, Austria, 2005. (conference article)

Master’s and doctoral theses

Matthias Samwald. “Semantic Web Technology in Neuroscience and Biomedicine. ” University of Vienna; Medical University of Vienna, 2007. (doctoral thesis)

Matthias Samwald. “Neuromuscular Synapses of the Sympathetic Nervous System” University of Vienna; Medical University of Vienna, 2005. (master’s thesis)

Articles published without peer-review

Jose Antonio Miñarro-Giménez, Oscar Marín-Alonso, and Matthias Samwald. “Applying Deep Learning Techniques on Medical Corpora from the World Wide Web: A Prototypical System and Evaluation.” arXiv:1502.03682 [cs], February 12, 2015. http://arxiv.org/abs/1502.03682.

Matthias Samwald. “Suchen und Finden” Das Österreichische Gesundheitswesen – ÖKZ, Ausgabe 52.JG 7, 2011. Article PDF

Alexandre Passant, Matthias Samwald, John G. Breslin, Stefan Decker. “Federating Distributed Social Data to Build an Interlinked Online Information Society.” IEEE Intelligent Systems 24, no. 6 (11, 2009): 44-48.

Holger Stenzhorn, Matthias Samwald. “Das Semantic Web als Werkzeug in der biomedizinischen Forschung.” In Social Semantic Web: Web 2.0 – Was nun? Heidelberg, Germany: Springer, 2009. (book chapter)

Matthias Samwald. “Extracting conclusion sections from PubMed abstracts for rapid key assertion integration in biomedical research” September 2009. Available from Nature Precedings: http://precedings.nature.com/documents/3775/version/1 (pre-print article)

Vipul Kashyap, Kei-Hoi Cheung, Donald Doherty, Matthias Samwald, M. Scott Marshall, Joanne Luciano, et al. “Ontology-Based Data Integration For Biomedical Research.” In The Semantic Web: Real-World Applications from Industry, 97-122, 2007. (book chapter)

Matthias Samwald.“Branchenreport: Semantische Technologien in den Life Sciences (Industry Report: Semantic Technologies in the Life Sciences).” Branchenreport der Semantic Web School. Vienna, Austria: Semantic Web School, 2007. (industry white paper)

Matthias Samwald. “Review: Dystroglycan in the Nervous System” June 2007. Available from Nature Precedings: http://precedings.nature.com/documents/196/version/1. (pre-print article)

Invited talks

Gere Sunder-Plassmann, Matthias Samwald“Making pharmacogenetic treatment optimization accessible across Europe”, held at the Transplant Forum of the Medical University of Vienna, October 27, Vienna, Austria.

Matthias Samwald.Semantic Technologies for Biomedical Decision Support, held at the EMBL-EBI Industry Programme Workshop, European Bioinformatics Institute, May 18, 2011, Hinxton/Cambridge, UK.

Matthias Samwald. “High-level knowledge representation on the Semantic Web: the Concept Web Alliance and related efforts”, held at the BioHackathon Symposium 2010, February 2010, Tokyo, Japan.

Matthias Samwald. “Scientific Information Integration”, held at the Hypotheses, Evidence and Relations (Hyp-ER) project meeting, May 2009, Elsevier Offices, Amsterdam, Netherlands.